{"entity": "researcher", "timestamp": "2026-07-12T08:58:18.942Z", "family": "P\u00e9rtille", "given": "Fabio", "initials": "F", "orcid": "0000-0002-7214-9184", "affiliations": ["Department of Physics, Chemistry and Biology, Link\u00f6ping University, SE-58183 Link\u00f6ping, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3"}}, "publications": [{"entity": "publication", "iuid": "9e4daf0046b8477fbc62333829667614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e4daf0046b8477fbc62333829667614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e4daf0046b8477fbc62333829667614"}}, "title": "Epigenetic changes as regulatory mechanism for the expression of life history stages in Zonotrichia capensis inhabiting an aseasonal environment", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Gonzalez\u2010 Gomez", "given": "Paulina L", "initials": "PL", "orcid": "0000-0002-1219-8881", "researcher": {"href": "https://publications.scilifelab.se/researcher/636c42cfcc1f46c4bc83ffaa6f99c597.json"}}, {"family": "Wingfield", "given": "John C", "initials": "JC"}, {"family": "Guerrero\u2010Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal-article", "published": "2026-05-00", "journal": {"title": "Journal of Avian Biology", "issn": "0908-8857", "volume": "2026", "issue": "3", "issn-l": null}, "abstract": null, "doi": "10.1002/jav.03516", "pmid": null, "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [], "notes": [], "created": "2026-06-01T11:10:53.812Z", "modified": "2026-06-01T11:10:54.000Z"}, {"entity": "publication", "iuid": "6af44bc75c7b4fe19763db841169ec45", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6af44bc75c7b4fe19763db841169ec45.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6af44bc75c7b4fe19763db841169ec45"}}, "title": "Genetic and neuro-epigenetic effects of divergent artificial selection for feather pecking behaviour in chickens.", "authors": [{"family": "de Haas", "given": "Elske N", "initials": "EN"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Kjaer", "given": "Joergen B", "initials": "JB"}, {"family": "Jensen", "given": "Per", "initials": "P", "orcid": "0000-0001-5491-0649", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83892cd7d6a46898629107a11205254.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal article", "published": "2024-12-19", "journal": {"title": "BMC Genomics", "issn": "1471-2164", "volume": "25", "issue": "1", "pages": "1219", "issn-l": "1471-2164"}, "abstract": "Feather pecking (FP) is a repetitive behaviour in chickens, influenced by genetic, epigenetic, and environmental factors, similar to behaviours seen in human developmental disorders (e.g., hyperactivity, autism). This study examines genetic and neuro-epigenetic factors in the thalamus of chickens from lines selected for seven generations for high or low FP behaviour (HFP or LFP). We integrate data on Differentially Methylated Regions (DMRs), Single Nucleotide Polymorphisms (SNPs), and Copy Number Variations (CNVs) in this controlled artificial selection process. Significant differences in behaviour, immunology, and neurology have been reported in these lines. We identified 710 SNPs in these lines that indicate new potentially important genes for FP such as TMPRSS6 (implicated in autism), and SST and ARNT2 (somatostatin function). CNV were the omic level most affected during selection. The largest CNVs found were in RIC3 (gain in HFP) and SH3RF2 (gain in LFP) genes, linked to nicotinic acetylcholine receptor regulation and human oncogenesis, respectively. Our study also suggests that promoters and introns are hotspots for CpG depletion. The overlapping of the omic levels investigated here with data from a public FP Quantitative Trait Loci (QTL) database revealed novel candidate genes for understanding repetitive behaviours, such as RTKN2, associated with Alzheimer's disease in humans. This study suggests CNVs as a crucial initial step for genomic diversification, potentially more impactful than SNPs.", "doi": "10.1186/s12864-024-11137-w", "pmid": "39702044", "labels": {"Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11657628"}, {"db": "pii", "key": "10.1186/s12864-024-11137-w"}], "notes": [], "created": "2025-02-28T14:22:16.646Z", "modified": "2025-04-07T07:29:14.100Z"}, {"entity": "publication", "iuid": "33b8258d3dae4c76bc38ea20958228dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33b8258d3dae4c76bc38ea20958228dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33b8258d3dae4c76bc38ea20958228dd"}}, "title": "Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model.", "authors": [{"family": "P\u00e9rtille", "given": "Fabio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Alvarez-Rodriguez", "given": "Manuel", "initials": "M", "orcid": "0000-0003-0120-354X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3a5fb294906a4207a70936f871a38835.json"}}, {"family": "da Silva", "given": "Arthur Nery", "initials": "AN", "orcid": "0000-0002-4668-9769", "researcher": {"href": "https://publications.scilifelab.se/researcher/728eb328ab4448bf98c4b81957bda020.json"}}, {"family": "Barranco", "given": "Isabel", "initials": "I", "orcid": "0000-0001-9873-814X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae7e0d86b5ee4056bf375d83e57b0f22.json"}}, {"family": "Roca", "given": "Jordi", "initials": "J", "orcid": "0000-0002-4213-3093", "researcher": {"href": "https://publications.scilifelab.se/researcher/de7704c544ae4dfb8789782bf33dcd24.json"}}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Rodriguez-Martinez", "given": "Heriberto", "initials": "H", "orcid": "0000-0002-5194-2124", "researcher": {"href": "https://publications.scilifelab.se/researcher/ebd20bf7b79844539931a1825391a3f7.json"}}], "type": "journal article", "published": "2021-03-06", "journal": {"title": "Int J Mol Sci", "issn": "1422-0067", "volume": "22", "issue": "5", "pages": "2679", "issn-l": null}, "abstract": "A combined Genotyping By Sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) protocol was used to identify-in parallel-genetic variation (Genomic-Wide Association Studies (GWAS) and epigenetic differences of Differentially Methylated Regions (DMR) in the genome of spermatozoa from the porcine animal model. Breeding boars with good semen quality (n = 11) and specific and well-documented differences in fertility (farrowing rate, FR) and prolificacy (litter size, LS) (n = 7) in artificial insemination programs, using combined FR and LS, were categorized as High Fertile (HF, n = 4) or Low Fertile (LF, n = 3), and boars with Unknown Fertility (UF, n = 4) were tested for eventual epigenetical similarity with those fertility-proven. We identified 165,944 Single Nucleotide Polymorphisms (SNPs) that explained 14-15% of variance among selection lines. Between HF and LF individuals (n = 7, 4 HF and 3 LF), we identified 169 SNPs with p \u2264 0.00015, which explained 58% of the variance. For the epigenetic analyses, we considered fertility and period of ejaculate collection (late-summer and mid-autumn). Approximately three times more DMRs were observed in HF than in LF boars across these periods. Interestingly, UF boars were clearly clustered with one of the other HF or LF groups. The highest differences in DMRs between HF and LF experimental groups across the pig genome were located in the chr 3, 9, 13, and 16, with most DMRs being hypermethylated in LF boars. In both HF and LF boars, DMRs were mostly hypermethylated in late-summer compared to mid-autumn. Three overlaps were detected between SNPs (p \u2264 0.0005, n = 1318) and CpG sites within DMRs. In conclusion, fertility levels in breeding males including FR and LS can be discerned using methylome analyses. The findings in this biomedical animal model ought to be applied besides sire selection for andrological diagnosis of idiopathic sub/infertility.", "doi": "10.3390/ijms22052679", "pmid": "33800945", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ijms22052679"}, {"db": "pmc", "key": "PMC7961483"}], "notes": [], "created": "2021-06-01T20:54:03.647Z", "modified": "2021-11-10T12:26:27.950Z"}, {"entity": "publication", "iuid": "9e62b2cc7c8f49ee82a29100eaf8594f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e62b2cc7c8f49ee82a29100eaf8594f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e62b2cc7c8f49ee82a29100eaf8594f"}}, "title": "DNA methylation in canine brains is related to domestication and dog-breed formation.", "authors": [{"family": "Sundman", "given": "Ann-Sofie", "initials": "AS"}, {"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Lehmann Coutinho", "given": "Luiz", "initials": "L"}, {"family": "Jazin", "given": "Elena", "initials": "E"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C"}, {"family": "Jensen", "given": "Per", "initials": "P", "orcid": "0000-0001-5491-0649", "researcher": {"href": "https://publications.scilifelab.se/researcher/b83892cd7d6a46898629107a11205254.json"}}], "type": "journal article", "published": "2020-10-29", "journal": {"title": "PLoS ONE", "issn": "1932-6203", "volume": "15", "issue": "10", "pages": "e0240787", "issn-l": "1932-6203"}, "abstract": "Epigenetic factors such as DNA methylation act as mediators in the interaction between genome and environment. Variation in the epigenome can both affect phenotype and be inherited, and epigenetics has been suggested to be an important factor in the evolutionary process. During domestication, dogs have evolved an unprecedented between-breed variation in morphology and behavior in an evolutionary short period. In the present study, we explore DNA methylation differences in brain, the most relevant tissue with respect to behavior, between wolf and dog breeds. We optimized a combined method of genotype-by-sequencing (GBS) and methylated DNA immunoprecipitation (MeDIP) for its application in canines. Genomic DNA from the frontal cortex of 38 dogs of 8 breeds and three wolves was used. GBS and GBS-MeDIP libraries were prepared and sequenced on Illuma HiSeq2500 platform. The reduced sample represented 1.18 \u00b1 0.4% of the total dog genome (2,4 billion BP), while the GBS-MeDIP covered 11,250,788 \u00b1 4,042,106 unique base pairs. We find substantial DNA methylation differences between wolf and dog and between the dog breeds. The methylation profiles of the different groups imply that epigenetic factors may have been important in the speciation from dog to wolf, but also in the divergence of different dog breeds. Specifically, we highlight methylation differences in genes related to behavior and morphology. We hypothesize that these differences are involved in the phenotypic variation found among dogs, whereas future studies will have to find the specific mechanisms. Our results not only add an intriguing new dimension to dog breeding but are also useful to further understanding of epigenetic involvement.", "doi": "10.1371/journal.pone.0240787", "pmid": "33119634", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-20-11468"}, {"db": "pmc", "key": "PMC7595415"}], "notes": [], "created": "2020-11-04T06:05:40.841Z", "modified": "2021-11-10T12:46:05.356Z"}, {"entity": "publication", "iuid": "93379f5a15c7458fac70fdb76edbaee8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/93379f5a15c7458fac70fdb76edbaee8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/93379f5a15c7458fac70fdb76edbaee8"}}, "title": "Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification.", "authors": [{"family": "P\u00e9rtille", "given": "F\u00e1bio", "initials": "F", "orcid": "0000-0002-7214-9184", "researcher": {"href": "https://publications.scilifelab.se/researcher/2279c5ebf16f419bab7c3af87bac81d3.json"}}, {"family": "Da Silva", "given": "Vinicius H", "initials": "VH"}, {"family": "Johansson", "given": "Anna M", "initials": "AM", "orcid": "0000-0002-9762-0497", "researcher": {"href": "https://publications.scilifelab.se/researcher/dbd1ea80ec964bc3ab675e84b27d17e6.json"}}, {"family": "Lindstr\u00f6m", "given": "Tom", "initials": "T", "orcid": "0000-0001-7856-2925", "researcher": {"href": "https://publications.scilifelab.se/researcher/1a619b495eed4a41a65f2bc7a3c7c5dc.json"}}, {"family": "Wright", "given": "Dominic", "initials": "D"}, {"family": "Coutinho", "given": "Luiz L", "initials": "LL"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Guerrero-Bosagna", "given": "Carlos", "initials": "C", "orcid": "0000-0003-1935-5875", "researcher": {"href": "https://publications.scilifelab.se/researcher/0175a0da7ca147d4a0430b085ed23669.json"}}], "type": "journal article", "published": "2019-07-00", "journal": {"volume": "14", "issn": "1559-2308", "issue": "7", "pages": "685-707", "title": "Epigenetics", "issn-l": "1559-2294"}, "abstract": "DNA methylation in CpGs dinucleotides is associated with high mutability and disappearance of CpG sites during evolution. Although the high mutability of CpGs is thought to be relevant for vertebrate evolution, very little is known on the role of CpG-related mutations in the genomic diversification of vertebrates. Our study analysed genetic differences in chickens, between Red Junglefowl (RJF; the living closest relative to the ancestor of domesticated chickens) and domesticated breeds, to identify genomic dynamics that have occurred during the process of their domestication, focusing particularly on CpG-related mutations. Single nucleotide polymorphisms (SNPs) and copy number variations (CNVs) between RJF and these domesticated breeds were assessed in a reduced fraction of their genome. Additionally, DNA methylation in the same fraction of the genome was measured in the sperm of RJF individuals to identify possible correlations with the mutations found between RJF and the domesticated breeds. Our study shows that although the vast majority of CpG-related mutations found relate to CNVs, CpGs disproportionally associate to SNPs in comparison to CNVs, where they are indeed substantially under-represented. Moreover, CpGs seem to be hotspots of mutations related to speciation. We suggest that, on the one hand, CpG-related mutations in CNV regions would promote genomic 'flexibility' in evolution, i.e., the ability of the genome to expand its functional possibilities; on the other hand, CpG-related mutations in SNPs would relate to genomic 'specificity' in evolution, thus, representing mutations that would associate with phenotypic traits relevant for speciation.", "doi": "10.1080/15592294.2019.1609868", "pmid": "31070073", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC6557589"}], "notes": [], "created": "2020-01-08T12:39:10.372Z", "modified": "2021-06-18T14:18:18.038Z"}]}